## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = FALSE, comment = "", fig.width = 7, fig.height = 4.6,
                      dev = if (knitr::is_latex_output()) "cairo_pdf" else
                        if (requireNamespace("svglite", quietly = TRUE)) "svglite" else "png")
if (requireNamespace("stability", quietly = TRUE)) library(stability) else
  pkgload::load_all(export_all = FALSE, helpers = FALSE, quiet = TRUE)


## ----reg----------------------------------------------------------------------
reg <-
  stab_reg(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
plot(x = reg, which = "lines")


## ----measures-----------------------------------------------------------------
sm <-
  stab_measures(
      .data = ge_data
    , .y    = Yield
    , .gen  = Gen
    , .env  = Env
    )
head(x = sm$StabMeasures[order(Ecov)], n = 6)
plot(x = sm, which = "ecov")


## ----measures-int-------------------------------------------------------------
stab_interpret(
    x             = sm
  , higher_better = TRUE
  , top           = 5
  )


## ----par----------------------------------------------------------------------
sp <-
  stab_par(
      .data   = ge_data
    , .y      = Yield
    , .rep    = Rep
    , .gen    = Gen
    , .env    = Env
    , alpha   = 0.1
    , .envCov = NULL
    )
sp$ANOVA
head(x = sp$SimultSel, n = 10)
plot(x = sp, which = "ys")


## ----par-int------------------------------------------------------------------
stab_interpret(
    x             = sp
  , higher_better = TRUE
  , top           = 5
  )


## ----ranks--------------------------------------------------------------------
kg <-
  stab_kang(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
head(x = kg$Kang, n = 6)
fx <-
  stab_fox(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
head(x = fx$Fox, n = 6)


## ----eskridge-----------------------------------------------------------------
es <-
  stab_eskridge(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    , alpha = 0.05
    )
head(x = es$Eskridge, n = 6)
round(x = es$RankCor, digits = 2)
plot(x = es, which = "ranks")
stab_interpret(
    x             = es
  , higher_better = TRUE
  , top           = 5
  )


## ----reliability--------------------------------------------------------------
rl <-
  stab_reliability(
      .data         = ge_data
    , .y            = Yield
    , .rep          = Rep
    , .gen          = Gen
    , .env          = Env
    , alpha         = 0.25
    , higher_better = TRUE
    )
head(x = rl$Reliability, n = 6)
su <-
  stab_superiority(
      .data         = ge_data
    , .y            = Yield
    , .rep          = Rep
    , .gen          = Gen
    , .env          = Env
    , higher_better = TRUE
    )
head(x = su$Superiority, n = 6)
plot(x = su)


## ----huehn--------------------------------------------------------------------
hu <-
  stab_huehn(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
head(x = hu$Huehn, n = 6)
hu$Tests
stab_interpret(
    x             = hu
  , higher_better = TRUE
  , top           = 5
  )